The definition of sepsis has been recently modified to accommodate emerging knowledge in the field, while at the same time being recognized as challenging, if not impossible, to define. Here we seek to clarify the current understanding of sepsis as one that has been typically framed as a disorder of inflammation to one in which the competing interests of the microbiota, pathobiota and host immune cells leads to loss of resilience and non-resolving organ dysfunction. Here we challenge the existence of the idea of non-infectious sepsis given that critically ill humans never exist in a germ free state. Finally, we propose a new vision of the pathophysiology of sepsis that includes the invariable loss of the host’s microbiome with the emergence of a pathobiome consisting of both healthcare acquired and healthcare adapted pathobiota. Under this framework, the critically ill patient is viewed as a host colonized by pathobiota dynamically expressing emergent properties which drive, and are driven by, a pathoadaptive immune response.